services/crunch-run/crunchrun.go

   1 package main
   2
   3 import (
   4         "encoding/json"
   5         "errors"
   6         "flag"
   7         "fmt"
   8         "git.curoverse.com/arvados.git/lib/crunchstat"
   9         "git.curoverse.com/arvados.git/sdk/go/arvados"
  10         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  11         "git.curoverse.com/arvados.git/sdk/go/keepclient"
  12         "git.curoverse.com/arvados.git/sdk/go/manifest"
  13         "github.com/curoverse/dockerclient"
  14         "io"
  15         "io/ioutil"
  16         "log"
  17         "os"
  18         "os/exec"
  19         "os/signal"
  20         "path"
  21         "path/filepath"
  22         "strings"
  23         "sync"
  24         "syscall"
  25         "time"
  26 )
  27
  28 // IArvadosClient is the minimal Arvados API methods used by crunch-run.
  29 type IArvadosClient interface {
  30         Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
  31         Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  32         Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
  33         Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
  34         Discovery(key string) (interface{}, error)
  35 }
  36
  37 // ErrCancelled is the error returned when the container is cancelled.
  38 var ErrCancelled = errors.New("Cancelled")
  39
  40 // IKeepClient is the minimal Keep API methods used by crunch-run.
  41 type IKeepClient interface {
  42         PutHB(hash string, buf []byte) (string, int, error)
  43         ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error)
  44 }
  45
  46 // NewLogWriter is a factory function to create a new log writer.
  47 type NewLogWriter func(name string) io.WriteCloser
  48
  49 type RunArvMount func(args []string, tok string) (*exec.Cmd, error)
  50
  51 type MkTempDir func(string, string) (string, error)
  52
  53 // ThinDockerClient is the minimal Docker client interface used by crunch-run.
  54 type ThinDockerClient interface {
  55         StopContainer(id string, timeout int) error
  56         InspectImage(id string) (*dockerclient.ImageInfo, error)
  57         LoadImage(reader io.Reader) error
  58         CreateContainer(config *dockerclient.ContainerConfig, name string, authConfig *dockerclient.AuthConfig) (string, error)
  59         StartContainer(id string, config *dockerclient.HostConfig) error
  60         AttachContainer(id string, options *dockerclient.AttachOptions) (io.ReadCloser, error)
  61         Wait(id string) <-chan dockerclient.WaitResult
  62         RemoveImage(name string, force bool) ([]*dockerclient.ImageDelete, error)
  63 }
  64
  65 // ContainerRunner is the main stateful struct used for a single execution of a
  66 // container.
  67 type ContainerRunner struct {
  68         Docker    ThinDockerClient
  69         ArvClient IArvadosClient
  70         Kc        IKeepClient
  71         arvados.Container
  72         dockerclient.ContainerConfig
  73         dockerclient.HostConfig
  74         token       string
  75         ContainerID string
  76         ExitCode    *int
  77         NewLogWriter
  78         loggingDone   chan bool
  79         CrunchLog     *ThrottledLogger
  80         Stdout        io.WriteCloser
  81         Stderr        *ThrottledLogger
  82         LogCollection *CollectionWriter
  83         LogsPDH       *string
  84         RunArvMount
  85         MkTempDir
  86         ArvMount       *exec.Cmd
  87         ArvMountPoint  string
  88         HostOutputDir  string
  89         CleanupTempDir []string
  90         Binds          []string
  91         OutputPDH      *string
  92         CancelLock     sync.Mutex
  93         Cancelled      bool
  94         SigChan        chan os.Signal
  95         ArvMountExit   chan error
  96         finalState     string
  97         trashLifetime  time.Duration
  98
  99         statLogger   io.WriteCloser
 100         statReporter *crunchstat.Reporter
 101         statInterval time.Duration
 102         cgroupRoot   string
 103         // What we expect the container's cgroup parent to be.
 104         expectCgroupParent string
 105         // What we tell docker to use as the container's cgroup
 106         // parent. Note: Ideally we would use the same field for both
 107         // expectCgroupParent and setCgroupParent, and just make it
 108         // default to "docker". However, when using docker < 1.10 with
 109         // systemd, specifying a non-empty cgroup parent (even the
 110         // default value "docker") hits a docker bug
 111         // (https://github.com/docker/docker/issues/17126). Using two
 112         // separate fields makes it possible to use the "expect cgroup
 113         // parent to be X" feature even on sites where the "specify
 114         // cgroup parent" feature breaks.
 115         setCgroupParent string
 116 }
 117
 118 // SetupSignals sets up signal handling to gracefully terminate the underlying
 119 // Docker container and update state when receiving a TERM, INT or QUIT signal.
 120 func (runner *ContainerRunner) SetupSignals() {
 121         runner.SigChan = make(chan os.Signal, 1)
 122         signal.Notify(runner.SigChan, syscall.SIGTERM)
 123         signal.Notify(runner.SigChan, syscall.SIGINT)
 124         signal.Notify(runner.SigChan, syscall.SIGQUIT)
 125
 126         go func(sig <-chan os.Signal) {
 127                 for range sig {
 128                         if !runner.Cancelled {
 129                                 runner.CancelLock.Lock()
 130                                 runner.Cancelled = true
 131                                 if runner.ContainerID != "" {
 132                                         runner.Docker.StopContainer(runner.ContainerID, 10)
 133                                 }
 134                                 runner.CancelLock.Unlock()
 135                         }
 136                 }
 137         }(runner.SigChan)
 138 }
 139
 140 // LoadImage determines the docker image id from the container record and
 141 // checks if it is available in the local Docker image store.  If not, it loads
 142 // the image from Keep.
 143 func (runner *ContainerRunner) LoadImage() (err error) {
 144
 145         runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
 146
 147         var collection arvados.Collection
 148         err = runner.ArvClient.Get("collections", runner.Container.ContainerImage, nil, &collection)
 149         if err != nil {
 150                 return fmt.Errorf("While getting container image collection: %v", err)
 151         }
 152         manifest := manifest.Manifest{Text: collection.ManifestText}
 153         var img, imageID string
 154         for ms := range manifest.StreamIter() {
 155                 img = ms.FileStreamSegments[0].Name
 156                 if !strings.HasSuffix(img, ".tar") {
 157                         return fmt.Errorf("First file in the container image collection does not end in .tar")
 158                 }
 159                 imageID = img[:len(img)-4]
 160         }
 161
 162         runner.CrunchLog.Printf("Using Docker image id '%s'", imageID)
 163
 164         _, err = runner.Docker.InspectImage(imageID)
 165         if err != nil {
 166                 runner.CrunchLog.Print("Loading Docker image from keep")
 167
 168                 var readCloser io.ReadCloser
 169                 readCloser, err = runner.Kc.ManifestFileReader(manifest, img)
 170                 if err != nil {
 171                         return fmt.Errorf("While creating ManifestFileReader for container image: %v", err)
 172                 }
 173
 174                 err = runner.Docker.LoadImage(readCloser)
 175                 if err != nil {
 176                         return fmt.Errorf("While loading container image into Docker: %v", err)
 177                 }
 178         } else {
 179                 runner.CrunchLog.Print("Docker image is available")
 180         }
 181
 182         runner.ContainerConfig.Image = imageID
 183
 184         return nil
 185 }
 186
 187 func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) (c *exec.Cmd, err error) {
 188         c = exec.Command("arv-mount", arvMountCmd...)
 189
 190         // Copy our environment, but override ARVADOS_API_TOKEN with
 191         // the container auth token.
 192         c.Env = nil
 193         for _, s := range os.Environ() {
 194                 if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
 195                         c.Env = append(c.Env, s)
 196                 }
 197         }
 198         c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
 199
 200         nt := NewThrottledLogger(runner.NewLogWriter("arv-mount"))
 201         c.Stdout = nt
 202         c.Stderr = nt
 203
 204         err = c.Start()
 205         if err != nil {
 206                 return nil, err
 207         }
 208
 209         statReadme := make(chan bool)
 210         runner.ArvMountExit = make(chan error)
 211
 212         keepStatting := true
 213         go func() {
 214                 for keepStatting {
 215                         time.Sleep(100 * time.Millisecond)
 216                         _, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
 217                         if err == nil {
 218                                 keepStatting = false
 219                                 statReadme <- true
 220                         }
 221                 }
 222                 close(statReadme)
 223         }()
 224
 225         go func() {
 226                 runner.ArvMountExit <- c.Wait()
 227                 close(runner.ArvMountExit)
 228         }()
 229
 230         select {
 231         case <-statReadme:
 232                 break
 233         case err := <-runner.ArvMountExit:
 234                 runner.ArvMount = nil
 235                 keepStatting = false
 236                 return nil, err
 237         }
 238
 239         return c, nil
 240 }
 241
 242 func (runner *ContainerRunner) SetupMounts() (err error) {
 243         runner.ArvMountPoint, err = runner.MkTempDir("", "keep")
 244         if err != nil {
 245                 return fmt.Errorf("While creating keep mount temp dir: %v", err)
 246         }
 247
 248         runner.CleanupTempDir = append(runner.CleanupTempDir, runner.ArvMountPoint)
 249
 250         pdhOnly := true
 251         tmpcount := 0
 252         arvMountCmd := []string{"--foreground", "--allow-other", "--read-write"}
 253         collectionPaths := []string{}
 254         runner.Binds = nil
 255
 256         for bind, mnt := range runner.Container.Mounts {
 257                 if bind == "stdout" {
 258                         // Is it a "file" mount kind?
 259                         if mnt.Kind != "file" {
 260                                 return fmt.Errorf("Unsupported mount kind '%s' for stdout. Only 'file' is supported.", mnt.Kind)
 261                         }
 262
 263                         // Does path start with OutputPath?
 264                         prefix := runner.Container.OutputPath
 265                         if !strings.HasSuffix(prefix, "/") {
 266                                 prefix += "/"
 267                         }
 268                         if !strings.HasPrefix(mnt.Path, prefix) {
 269                                 return fmt.Errorf("Stdout path does not start with OutputPath: %s, %s", mnt.Path, prefix)
 270                         }
 271                 }
 272
 273                 switch {
 274                 case mnt.Kind == "collection":
 275                         var src string
 276                         if mnt.UUID != "" && mnt.PortableDataHash != "" {
 277                                 return fmt.Errorf("Cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
 278                         }
 279                         if mnt.UUID != "" {
 280                                 if mnt.Writable {
 281                                         return fmt.Errorf("Writing to existing collections currently not permitted.")
 282                                 }
 283                                 pdhOnly = false
 284                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
 285                         } else if mnt.PortableDataHash != "" {
 286                                 if mnt.Writable {
 287                                         return fmt.Errorf("Can never write to a collection specified by portable data hash")
 288                                 }
 289                                 src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
 290                         } else {
 291                                 src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
 292                                 arvMountCmd = append(arvMountCmd, "--mount-tmp")
 293                                 arvMountCmd = append(arvMountCmd, fmt.Sprintf("tmp%d", tmpcount))
 294                                 tmpcount += 1
 295                         }
 296                         if mnt.Writable {
 297                                 if bind == runner.Container.OutputPath {
 298                                         runner.HostOutputDir = src
 299                                 }
 300                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind))
 301                         } else {
 302                                 runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", src, bind))
 303                         }
 304                         collectionPaths = append(collectionPaths, src)
 305
 306                 case mnt.Kind == "tmp" && bind == runner.Container.OutputPath:
 307                         runner.HostOutputDir, err = runner.MkTempDir("", "")
 308                         if err != nil {
 309                                 return fmt.Errorf("While creating mount temp dir: %v", err)
 310                         }
 311                         st, staterr := os.Stat(runner.HostOutputDir)
 312                         if staterr != nil {
 313                                 return fmt.Errorf("While Stat on temp dir: %v", staterr)
 314                         }
 315                         err = os.Chmod(runner.HostOutputDir, st.Mode()|os.ModeSetgid|0777)
 316                         if staterr != nil {
 317                                 return fmt.Errorf("While Chmod temp dir: %v", err)
 318                         }
 319                         runner.CleanupTempDir = append(runner.CleanupTempDir, runner.HostOutputDir)
 320                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", runner.HostOutputDir, bind))
 321
 322                 case mnt.Kind == "tmp":
 323                         runner.Binds = append(runner.Binds, bind)
 324
 325                 case mnt.Kind == "json":
 326                         jsondata, err := json.Marshal(mnt.Content)
 327                         if err != nil {
 328                                 return fmt.Errorf("encoding json data: %v", err)
 329                         }
 330                         // Create a tempdir with a single file
 331                         // (instead of just a tempfile): this way we
 332                         // can ensure the file is world-readable
 333                         // inside the container, without having to
 334                         // make it world-readable on the docker host.
 335                         tmpdir, err := runner.MkTempDir("", "")
 336                         if err != nil {
 337                                 return fmt.Errorf("creating temp dir: %v", err)
 338                         }
 339                         runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 340                         tmpfn := filepath.Join(tmpdir, "mountdata.json")
 341                         err = ioutil.WriteFile(tmpfn, jsondata, 0644)
 342                         if err != nil {
 343                                 return fmt.Errorf("writing temp file: %v", err)
 344                         }
 345                         runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s:ro", tmpfn, bind))
 346                 }
 347         }
 348
 349         if runner.HostOutputDir == "" {
 350                 return fmt.Errorf("Output path does not correspond to a writable mount point")
 351         }
 352
 353         if pdhOnly {
 354                 arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id")
 355         } else {
 356                 arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
 357         }
 358         arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
 359
 360         token, err := runner.ContainerToken()
 361         if err != nil {
 362                 return fmt.Errorf("could not get container token: %s", err)
 363         }
 364
 365         runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
 366         if err != nil {
 367                 return fmt.Errorf("While trying to start arv-mount: %v", err)
 368         }
 369
 370         for _, p := range collectionPaths {
 371                 _, err = os.Stat(p)
 372                 if err != nil {
 373                         return fmt.Errorf("While checking that input files exist: %v", err)
 374                 }
 375         }
 376
 377         return nil
 378 }
 379
 380 func (runner *ContainerRunner) ProcessDockerAttach(containerReader io.Reader) {
 381         // Handle docker log protocol
 382         // https://docs.docker.com/engine/reference/api/docker_remote_api_v1.15/#attach-to-a-container
 383
 384         header := make([]byte, 8)
 385         for {
 386                 _, readerr := io.ReadAtLeast(containerReader, header, 8)
 387
 388                 if readerr == nil {
 389                         readsize := int64(header[7]) | (int64(header[6]) << 8) | (int64(header[5]) << 16) | (int64(header[4]) << 24)
 390                         if header[0] == 1 {
 391                                 // stdout
 392                                 _, readerr = io.CopyN(runner.Stdout, containerReader, readsize)
 393                         } else {
 394                                 // stderr
 395                                 _, readerr = io.CopyN(runner.Stderr, containerReader, readsize)
 396                         }
 397                 }
 398
 399                 if readerr != nil {
 400                         if readerr != io.EOF {
 401                                 runner.CrunchLog.Printf("While reading docker logs: %v", readerr)
 402                         }
 403
 404                         closeerr := runner.Stdout.Close()
 405                         if closeerr != nil {
 406                                 runner.CrunchLog.Printf("While closing stdout logs: %v", closeerr)
 407                         }
 408
 409                         closeerr = runner.Stderr.Close()
 410                         if closeerr != nil {
 411                                 runner.CrunchLog.Printf("While closing stderr logs: %v", closeerr)
 412                         }
 413
 414                         if runner.statReporter != nil {
 415                                 runner.statReporter.Stop()
 416                                 closeerr = runner.statLogger.Close()
 417                                 if closeerr != nil {
 418                                         runner.CrunchLog.Printf("While closing crunchstat logs: %v", closeerr)
 419                                 }
 420                         }
 421
 422                         runner.loggingDone <- true
 423                         close(runner.loggingDone)
 424                         return
 425                 }
 426         }
 427 }
 428
 429 func (runner *ContainerRunner) StartCrunchstat() {
 430         runner.statLogger = NewThrottledLogger(runner.NewLogWriter("crunchstat"))
 431         runner.statReporter = &crunchstat.Reporter{
 432                 CID:          runner.ContainerID,
 433                 Logger:       log.New(runner.statLogger, "", 0),
 434                 CgroupParent: runner.expectCgroupParent,
 435                 CgroupRoot:   runner.cgroupRoot,
 436                 PollPeriod:   runner.statInterval,
 437         }
 438         runner.statReporter.Start()
 439 }
 440
 441 // AttachLogs connects the docker container stdout and stderr logs to the
 442 // Arvados logger which logs to Keep and the API server logs table.
 443 func (runner *ContainerRunner) AttachStreams() (err error) {
 444
 445         runner.CrunchLog.Print("Attaching container streams")
 446
 447         var containerReader io.Reader
 448         containerReader, err = runner.Docker.AttachContainer(runner.ContainerID,
 449                 &dockerclient.AttachOptions{Stream: true, Stdout: true, Stderr: true})
 450         if err != nil {
 451                 return fmt.Errorf("While attaching container stdout/stderr streams: %v", err)
 452         }
 453
 454         runner.loggingDone = make(chan bool)
 455
 456         if stdoutMnt, ok := runner.Container.Mounts["stdout"]; ok {
 457                 stdoutPath := stdoutMnt.Path[len(runner.Container.OutputPath):]
 458                 index := strings.LastIndex(stdoutPath, "/")
 459                 if index > 0 {
 460                         subdirs := stdoutPath[:index]
 461                         if subdirs != "" {
 462                                 st, err := os.Stat(runner.HostOutputDir)
 463                                 if err != nil {
 464                                         return fmt.Errorf("While Stat on temp dir: %v", err)
 465                                 }
 466                                 stdoutPath := path.Join(runner.HostOutputDir, subdirs)
 467                                 err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
 468                                 if err != nil {
 469                                         return fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
 470                                 }
 471                         }
 472                 }
 473                 stdoutFile, err := os.Create(path.Join(runner.HostOutputDir, stdoutPath))
 474                 if err != nil {
 475                         return fmt.Errorf("While creating stdout file: %v", err)
 476                 }
 477                 runner.Stdout = stdoutFile
 478         } else {
 479                 runner.Stdout = NewThrottledLogger(runner.NewLogWriter("stdout"))
 480         }
 481         runner.Stderr = NewThrottledLogger(runner.NewLogWriter("stderr"))
 482
 483         go runner.ProcessDockerAttach(containerReader)
 484
 485         return nil
 486 }
 487
 488 // CreateContainer creates the docker container.
 489 func (runner *ContainerRunner) CreateContainer() error {
 490         runner.CrunchLog.Print("Creating Docker container")
 491
 492         runner.ContainerConfig.Cmd = runner.Container.Command
 493         if runner.Container.Cwd != "." {
 494                 runner.ContainerConfig.WorkingDir = runner.Container.Cwd
 495         }
 496
 497         for k, v := range runner.Container.Environment {
 498                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env, k+"="+v)
 499         }
 500         if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
 501                 tok, err := runner.ContainerToken()
 502                 if err != nil {
 503                         return err
 504                 }
 505                 runner.ContainerConfig.Env = append(runner.ContainerConfig.Env,
 506                         "ARVADOS_API_TOKEN="+tok,
 507                         "ARVADOS_API_HOST="+os.Getenv("ARVADOS_API_HOST"),
 508                         "ARVADOS_API_HOST_INSECURE="+os.Getenv("ARVADOS_API_HOST_INSECURE"),
 509                 )
 510                 runner.ContainerConfig.NetworkDisabled = false
 511         } else {
 512                 runner.ContainerConfig.NetworkDisabled = true
 513         }
 514
 515         var err error
 516         runner.ContainerID, err = runner.Docker.CreateContainer(&runner.ContainerConfig, "", nil)
 517         if err != nil {
 518                 return fmt.Errorf("While creating container: %v", err)
 519         }
 520
 521         runner.HostConfig = dockerclient.HostConfig{
 522                 Binds:        runner.Binds,
 523                 CgroupParent: runner.setCgroupParent,
 524                 LogConfig: dockerclient.LogConfig{
 525                         Type: "none",
 526                 },
 527         }
 528
 529         return runner.AttachStreams()
 530 }
 531
 532 // StartContainer starts the docker container created by CreateContainer.
 533 func (runner *ContainerRunner) StartContainer() error {
 534         runner.CrunchLog.Printf("Starting Docker container id '%s'", runner.ContainerID)
 535         err := runner.Docker.StartContainer(runner.ContainerID, &runner.HostConfig)
 536         if err != nil {
 537                 return fmt.Errorf("could not start container: %v", err)
 538         }
 539         return nil
 540 }
 541
 542 // WaitFinish waits for the container to terminate, capture the exit code, and
 543 // close the stdout/stderr logging.
 544 func (runner *ContainerRunner) WaitFinish() error {
 545         runner.CrunchLog.Print("Waiting for container to finish")
 546
 547         result := runner.Docker.Wait(runner.ContainerID)
 548         wr := <-result
 549         if wr.Error != nil {
 550                 return fmt.Errorf("While waiting for container to finish: %v", wr.Error)
 551         }
 552         runner.ExitCode = &wr.ExitCode
 553
 554         // wait for stdout/stderr to complete
 555         <-runner.loggingDone
 556
 557         return nil
 558 }
 559
 560 // HandleOutput sets the output, unmounts the FUSE mount, and deletes temporary directories
 561 func (runner *ContainerRunner) CaptureOutput() error {
 562         if runner.finalState != "Complete" {
 563                 return nil
 564         }
 565
 566         if runner.HostOutputDir == "" {
 567                 return nil
 568         }
 569
 570         _, err := os.Stat(runner.HostOutputDir)
 571         if err != nil {
 572                 return fmt.Errorf("While checking host output path: %v", err)
 573         }
 574
 575         var manifestText string
 576
 577         collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
 578         _, err = os.Stat(collectionMetafile)
 579         if err != nil {
 580                 // Regular directory
 581                 cw := CollectionWriter{runner.Kc, nil, sync.Mutex{}}
 582                 manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
 583                 if err != nil {
 584                         return fmt.Errorf("While uploading output files: %v", err)
 585                 }
 586         } else {
 587                 // FUSE mount directory
 588                 file, openerr := os.Open(collectionMetafile)
 589                 if openerr != nil {
 590                         return fmt.Errorf("While opening FUSE metafile: %v", err)
 591                 }
 592                 defer file.Close()
 593
 594                 var rec arvados.Collection
 595                 err = json.NewDecoder(file).Decode(&rec)
 596                 if err != nil {
 597                         return fmt.Errorf("While reading FUSE metafile: %v", err)
 598                 }
 599                 manifestText = rec.ManifestText
 600         }
 601
 602         var response arvados.Collection
 603         err = runner.ArvClient.Create("collections",
 604                 arvadosclient.Dict{
 605                         "collection": arvadosclient.Dict{
 606                                 "expires_at":    time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
 607                                 "name":          "output for " + runner.Container.UUID,
 608                                 "manifest_text": manifestText}},
 609                 &response)
 610         if err != nil {
 611                 return fmt.Errorf("While creating output collection: %v", err)
 612         }
 613         runner.OutputPDH = &response.PortableDataHash
 614         return nil
 615 }
 616
 617 func (runner *ContainerRunner) loadDiscoveryVars() {
 618         tl, err := runner.ArvClient.Discovery("defaultTrashLifetime")
 619         if err != nil {
 620                 log.Fatalf("getting defaultTrashLifetime from discovery document: %s", err)
 621         }
 622         runner.trashLifetime = time.Duration(tl.(float64)) * time.Second
 623 }
 624
 625 func (runner *ContainerRunner) CleanupDirs() {
 626         if runner.ArvMount != nil {
 627                 umount := exec.Command("fusermount", "-z", "-u", runner.ArvMountPoint)
 628                 umnterr := umount.Run()
 629                 if umnterr != nil {
 630                         runner.CrunchLog.Printf("While running fusermount: %v", umnterr)
 631                 }
 632
 633                 mnterr := <-runner.ArvMountExit
 634                 if mnterr != nil {
 635                         runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
 636                 }
 637         }
 638
 639         for _, tmpdir := range runner.CleanupTempDir {
 640                 rmerr := os.RemoveAll(tmpdir)
 641                 if rmerr != nil {
 642                         runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", tmpdir, rmerr)
 643                 }
 644         }
 645 }
 646
 647 // CommitLogs posts the collection containing the final container logs.
 648 func (runner *ContainerRunner) CommitLogs() error {
 649         runner.CrunchLog.Print(runner.finalState)
 650         runner.CrunchLog.Close()
 651
 652         // Closing CrunchLog above allows it to be committed to Keep at this
 653         // point, but re-open crunch log with ArvClient in case there are any
 654         // other further (such as failing to write the log to Keep!) while
 655         // shutting down
 656         runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{runner.ArvClient, runner.Container.UUID,
 657                 "crunch-run", nil})
 658
 659         if runner.LogsPDH != nil {
 660                 // If we have already assigned something to LogsPDH,
 661                 // we must be closing the re-opened log, which won't
 662                 // end up getting attached to the container record and
 663                 // therefore doesn't need to be saved as a collection
 664                 // -- it exists only to send logs to other channels.
 665                 return nil
 666         }
 667
 668         mt, err := runner.LogCollection.ManifestText()
 669         if err != nil {
 670                 return fmt.Errorf("While creating log manifest: %v", err)
 671         }
 672
 673         var response arvados.Collection
 674         err = runner.ArvClient.Create("collections",
 675                 arvadosclient.Dict{
 676                         "collection": arvadosclient.Dict{
 677                                 "expires_at":    time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
 678                                 "name":          "logs for " + runner.Container.UUID,
 679                                 "manifest_text": mt}},
 680                 &response)
 681         if err != nil {
 682                 return fmt.Errorf("While creating log collection: %v", err)
 683         }
 684         runner.LogsPDH = &response.PortableDataHash
 685         return nil
 686 }
 687
 688 // UpdateContainerRunning updates the container state to "Running"
 689 func (runner *ContainerRunner) UpdateContainerRunning() error {
 690         runner.CancelLock.Lock()
 691         defer runner.CancelLock.Unlock()
 692         if runner.Cancelled {
 693                 return ErrCancelled
 694         }
 695         return runner.ArvClient.Update("containers", runner.Container.UUID,
 696                 arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running"}}, nil)
 697 }
 698
 699 // ContainerToken returns the api_token the container (and any
 700 // arv-mount processes) are allowed to use.
 701 func (runner *ContainerRunner) ContainerToken() (string, error) {
 702         if runner.token != "" {
 703                 return runner.token, nil
 704         }
 705
 706         var auth arvados.APIClientAuthorization
 707         err := runner.ArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
 708         if err != nil {
 709                 return "", err
 710         }
 711         runner.token = auth.APIToken
 712         return runner.token, nil
 713 }
 714
 715 // UpdateContainerComplete updates the container record state on API
 716 // server to "Complete" or "Cancelled"
 717 func (runner *ContainerRunner) UpdateContainerFinal() error {
 718         update := arvadosclient.Dict{}
 719         update["state"] = runner.finalState
 720         if runner.finalState == "Complete" {
 721                 if runner.LogsPDH != nil {
 722                         update["log"] = *runner.LogsPDH
 723                 }
 724                 if runner.ExitCode != nil {
 725                         update["exit_code"] = *runner.ExitCode
 726                 }
 727                 if runner.OutputPDH != nil {
 728                         update["output"] = *runner.OutputPDH
 729                 }
 730         }
 731         return runner.ArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
 732 }
 733
 734 // IsCancelled returns the value of Cancelled, with goroutine safety.
 735 func (runner *ContainerRunner) IsCancelled() bool {
 736         runner.CancelLock.Lock()
 737         defer runner.CancelLock.Unlock()
 738         return runner.Cancelled
 739 }
 740
 741 // NewArvLogWriter creates an ArvLogWriter
 742 func (runner *ContainerRunner) NewArvLogWriter(name string) io.WriteCloser {
 743         return &ArvLogWriter{runner.ArvClient, runner.Container.UUID, name, runner.LogCollection.Open(name + ".txt")}
 744 }
 745
 746 // Run the full container lifecycle.
 747 func (runner *ContainerRunner) Run() (err error) {
 748         runner.CrunchLog.Printf("Executing container '%s'", runner.Container.UUID)
 749
 750         hostname, hosterr := os.Hostname()
 751         if hosterr != nil {
 752                 runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
 753         } else {
 754                 runner.CrunchLog.Printf("Executing on host '%s'", hostname)
 755         }
 756
 757         // Clean up temporary directories _after_ finalizing
 758         // everything (if we've made any by then)
 759         defer runner.CleanupDirs()
 760
 761         runner.finalState = "Queued"
 762
 763         defer func() {
 764                 // checkErr prints e (unless it's nil) and sets err to
 765                 // e (unless err is already non-nil). Thus, if err
 766                 // hasn't already been assigned when Run() returns,
 767                 // this cleanup func will cause Run() to return the
 768                 // first non-nil error that is passed to checkErr().
 769                 checkErr := func(e error) {
 770                         if e == nil {
 771                                 return
 772                         }
 773                         runner.CrunchLog.Print(e)
 774                         if err == nil {
 775                                 err = e
 776                         }
 777                 }
 778
 779                 // Log the error encountered in Run(), if any
 780                 checkErr(err)
 781
 782                 if runner.finalState == "Queued" {
 783                         runner.UpdateContainerFinal()
 784                         return
 785                 }
 786
 787                 if runner.IsCancelled() {
 788                         runner.finalState = "Cancelled"
 789                         // but don't return yet -- we still want to
 790                         // capture partial output and write logs
 791                 }
 792
 793                 checkErr(runner.CaptureOutput())
 794                 checkErr(runner.CommitLogs())
 795                 checkErr(runner.UpdateContainerFinal())
 796
 797                 // The real log is already closed, but then we opened
 798                 // a new one in case we needed to log anything while
 799                 // finalizing.
 800                 runner.CrunchLog.Close()
 801         }()
 802
 803         err = runner.ArvClient.Get("containers", runner.Container.UUID, nil, &runner.Container)
 804         if err != nil {
 805                 err = fmt.Errorf("While getting container record: %v", err)
 806                 return
 807         }
 808
 809         // setup signal handling
 810         runner.SetupSignals()
 811
 812         // check for and/or load image
 813         err = runner.LoadImage()
 814         if err != nil {
 815                 err = fmt.Errorf("While loading container image: %v", err)
 816                 return
 817         }
 818
 819         // set up FUSE mount and binds
 820         err = runner.SetupMounts()
 821         if err != nil {
 822                 err = fmt.Errorf("While setting up mounts: %v", err)
 823                 return
 824         }
 825
 826         err = runner.CreateContainer()
 827         if err != nil {
 828                 return
 829         }
 830
 831         runner.StartCrunchstat()
 832
 833         if runner.IsCancelled() {
 834                 return
 835         }
 836
 837         err = runner.UpdateContainerRunning()
 838         if err != nil {
 839                 return
 840         }
 841         runner.finalState = "Cancelled"
 842
 843         err = runner.StartContainer()
 844         if err != nil {
 845                 return
 846         }
 847
 848         err = runner.WaitFinish()
 849         if err == nil {
 850                 runner.finalState = "Complete"
 851         }
 852         return
 853 }
 854
 855 // NewContainerRunner creates a new container runner.
 856 func NewContainerRunner(api IArvadosClient,
 857         kc IKeepClient,
 858         docker ThinDockerClient,
 859         containerUUID string) *ContainerRunner {
 860
 861         cr := &ContainerRunner{ArvClient: api, Kc: kc, Docker: docker}
 862         cr.NewLogWriter = cr.NewArvLogWriter
 863         cr.RunArvMount = cr.ArvMountCmd
 864         cr.MkTempDir = ioutil.TempDir
 865         cr.LogCollection = &CollectionWriter{kc, nil, sync.Mutex{}}
 866         cr.Container.UUID = containerUUID
 867         cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
 868         cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
 869         cr.loadDiscoveryVars()
 870         return cr
 871 }
 872
 873 func main() {
 874         statInterval := flag.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
 875         cgroupRoot := flag.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
 876         cgroupParent := flag.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
 877         cgroupParentSubsystem := flag.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
 878         flag.Parse()
 879
 880         containerId := flag.Arg(0)
 881
 882         api, err := arvadosclient.MakeArvadosClient()
 883         if err != nil {
 884                 log.Fatalf("%s: %v", containerId, err)
 885         }
 886         api.Retries = 8
 887
 888         var kc *keepclient.KeepClient
 889         kc, err = keepclient.MakeKeepClient(api)
 890         if err != nil {
 891                 log.Fatalf("%s: %v", containerId, err)
 892         }
 893         kc.Retries = 4
 894
 895         var docker *dockerclient.DockerClient
 896         docker, err = dockerclient.NewDockerClient("unix:///var/run/docker.sock", nil)
 897         if err != nil {
 898                 log.Fatalf("%s: %v", containerId, err)
 899         }
 900
 901         cr := NewContainerRunner(api, kc, docker, containerId)
 902         cr.statInterval = *statInterval
 903         cr.cgroupRoot = *cgroupRoot
 904         cr.expectCgroupParent = *cgroupParent
 905         if *cgroupParentSubsystem != "" {
 906                 p := findCgroup(*cgroupParentSubsystem)
 907                 cr.setCgroupParent = p
 908                 cr.expectCgroupParent = p
 909         }
 910
 911         err = cr.Run()
 912         if err != nil {
 913                 log.Fatalf("%s: %v", containerId, err)
 914         }
 915
 916 }